<p>Molybdenum (Mo) can substitute for nickel (Ni) to effectively lower the ductile-brittle transition temperature of EH420 ship plate steel. However, the mechanisms underlying the formation and evolution of inclusions in this new alloy system remain poorly understood, which is critical for developing the deoxidation alloying process for molten steel. This study focused on Mg-treated EH420 ship plate steel, analyzing the evolution of inclusions in different alloy systems containing either Ni or Mo and their effects on microstructure. The findings revealed that in both systems, alumina inclusions in the steel transformed into typical composite inclusions, characterized by Mg–Al–O spinel or Mg–Al–Ti–O cores enveloped by MnS in the outer layer following Mg treatment. Notably, the average size of the modified inclusions decreased significantly, while the quantity of smaller inclusions increased, particularly in the Mo–Mg system. At the microstructural level, the refinement effect of the rolled microstructure in the Mo–Mg system is optimal. Analysis using Factsage thermodynamic software indicates that the temperature range of the stable phase during the solidification process in the Mo–Mg system has expanded. This broadening may primarily account for the differences in inclusion evolution observed between the two alloy systems. Furthermore, during the solidification of molten steel in this system, the precipitation of carbides at the grain boundaries refines the austenite grains, thereby enhancing the microstructure. This study highlights the potential of Mg–Mo synergy in improving the microstructure and properties of ship plate steel, offering a theoretical foundation for the inclusion engineering of high-strength ship plate steel.</p>